________________________________ From: Mark Abraham <mark.abra...@anu.edu.au> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Friday, January 28, 2011 17:51:41 Subject: Re: [gmx-users] invacuo simulation On 28/01/2011 8:45 PM, Kwee Hong wrote: Hi > > In John's "GROMACS tutorial for solvation study of spider toxin peptide",I keep on getting an error message at the production stage: > > >Step 12111 Warning: Pressure scaling more than 1%. > >Step 12121 Warning: Pressure scaling more than 1%. > >Step 12131 Warning: Pressure scaling more than 1%. > >------------------------------------------------------- >Program mdrun, VERSION 4.5.1 >Source code file: ns.c, line: 2544 > >Fatal error: >One of the box vectors has become shorter than twice the cut-off >length or box_yy-|box_zy| or box_zz has become smaller than the >cut-off. >For more information and tips for troubleshooting, please check the >GROMACS >website at http://www.gromacs.org/Documentation/Errors > >I've tried a few approaches after reading the mailing list yet I'm >still getting the same error message. > >The command lined I used in this simulation is as follow: >pdb2gmx -ignh -ff gtomos43a1 -f 1OMB.pdb -o fws.pdb -p fws.top >-water >spce > Typo there. Sorry for the typo editconf -bt cubic -f fws.pdb -o fws.pdb -d 1.0 >grompp -f em.mdp -c fws.pdb -p fws.top -o em.tpr -maxwarn 5 >mdrun -v -deffnm em >grompp -f md.mdp -c em.gro -p fws.top -o md.tpr -maxwarn 3 >mdrun -v -deffnm md > Look at those warnings. Unless you know what they are and why ignoring them is OK, don't use -maxwarn. There is actually no warning but note: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing I think this is not significant since I'm running the simulation on single workstation. >After getting the error above round step 2300, I increased the tau_p >from 0.5 to 1.0. > >Yet I got the same error message at step 5400 though the warning on >pressure scaling more than 1% was gone. > >Therefore, I inceased the -d option in editconf to 1.5. > >But once again, I got the same error message at step 7300 (no >warning >on pressure scaling). > >So once again, I increased the -d option in editconf to 2.5. > >And I still got the same error message at step 11300. > >I'm now real lost in solving this.. I hereby attach my full.mdp >file, >hopefully to get some insight here. >Any suggestions are appreciated. > .mdp file looks OK. Mark >Thanks. > >Regards, >Joyce > > > >
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists